Monday, 12 August 2019

Version 2.99_005 released, Version 3 is next

The final development release in the 2.99 series has now been released (2.99_005).

Barring any major issues, this will be the final development release before Version 3 is released.


The main update in this version (from 2.99_004) is that the spatial patterns of cluster and region grower analysis outputs can now be exported to shapefile format, with each branch getting its own polygon or point features.  This means you can now use the polygon or point geometries for any branch in the tree for further analysis and/or display.  More details are in the blog post:  https://biodiverse-analysis-software.blogspot.com/2019/08/export-cluster-analyses-to-shapefiles.html


The more detailed summary of changes in the 2.99 series is at https://github.com/shawnlaffan/biodiverse/wiki/ReleaseNotes#version-299, and the related blog posts can be accessed via https://biodiverse-analysis-software.blogspot.com/search/label/Version3


This version can be downloaded from links on the downloads page at https://github.com/shawnlaffan/biodiverse/wiki/Downloads


Shawn Laffan
12-August-2019


--------

For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse


To see what Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList



You can also join the Biodiverse-users mailing list at http://groups.google.com/group/Biodiverse-users

Export cluster analyses to shapefiles

In Version 3 of Biodiverse it is possible to export your cluster and region grower analyses to shapefile formats.

This makes it easier to use the regions in geospatial analyses, for example as conditions in spatial analyses in Biodiverse.  Perhaps the best example is that you can generate a regionalisation using one data set, and then assess its values for one or more other data sets.  See for example Gonz├ílez-Orozco et al. (2013, 2014a and 2014b).

The option is available via the export menu for cluster and region grower analyses.  The options are all the usual ones, although that is not many in this case.


The option is chosen from the export menu for a cluster (or region grower) analysis.  


There are not that many choices, but Shape type can be exported as POLYGON or POINT geometries (shapes).  You can attach lists of results, or choose to only export the geometries themselves.


You might need to run a selection to highlight the branch you are interested in.  This example is branch 120___, which corresponds to the red cluster in the first screenshot above.  You might also choose to use a Definition Query (ArcGIS) or Layer Subset (QGIS) to filter out the geometries you are not interested in.  


And here the component polygons that form the polygons for branch 120___ are highlighted in red.



There are three points to watch for.

1.  If you export a list with the data, then each polygon or point feature is repeated for each item in the list.  This is due to shapefile field names being limited to 11 characters, which is far too short for many of the list entries in Biodiverse.  (Support for the GeoPackage format is in the works to obviate this issue).

2.  The exported features (geometries) are multipolygon or multipoint.  This means that each geometry comprises one or more geometries, with each internal branch including all polygons of its terminal branches.  The internal boundaries between polygons are not dissolved, so you will see all the component polygons, but any GIS will support a dissolve operation.  If you are wondering what multipolygons and multipoints are, then Wikipedia has a decent explanation as part of the Well Known Text entry.

3.  Remember that Biodiverse knows nothing about coordinate systems and map projections (agnostic might be a better way of putting it).  You will need to define the coordinate system of the output file yourself using a GIS or other geospatial tool.



Shawn Laffan
12-August-2019

If you want to try this out before version 3 is released then the 2.99_005 development release can be accessed through the downloads page at https://github.com/shawnlaffan/biodiverse/wiki/Downloads


--------

For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse


To see what Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList



You can also join the Biodiverse-users mailing list at http://groups.google.com/group/Biodiverse-users